BN1726 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 2 5.9099e-07 5.8889e-04
Layer 3 7.2293e-07 5.4554e-04
Layer 4 2.2404e-06 1.1695e-04
Layer 5 1.1452e-04 9.0737e-04
Layer 6 1.9780e-04 3.8952e-03
WM 2.2386e-01 3.1608e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.1094 0.7753
GABRG2 Layer 4 2.9668 0.7665
MAPK10 Layer 4 2.6719 0.7523
SERPINI1 Layer 4 2.5000 0.7511
STMN2 Layer 5 2.4668 0.7499
NAP1L2 Layer 4 2.4785 0.7498
CABP1 Layer 4 2.5000 0.7493
CPLX1 Layer 4 2.5176 0.7493
ATP2B2 Layer 4 2.7480 0.7490
NDRG4 Layer 4 2.5957 0.7484
SLC12A5 Layer 2 2.7422 0.7480
SV2A Layer 3 2.5449 0.7476
CAMK2A Layer 2 2.8906 0.7475
GABRA1 Layer 4 2.7480 0.7474
PRKAR1B Layer 5 2.3555 0.7471
SNCB Layer 4 2.4023 0.7448
PAFAH1B1 Layer 5 2.3184 0.7421
ATP1A1 Layer 2 2.5029 0.7401
BEX5 Layer 4 2.7656 0.7400
RAB3A Layer 4 2.3926 0.7396
CPLX2 Layer 2 2.5449 0.7391
NRN1 Layer 4 2.7598 0.7391
NCDN Layer 2 2.6016 0.7390
GPI Layer 4 2.4082 0.7370
CEND1 Layer 4 2.7070 0.7367
GAP43 Layer 3 2.2461 0.7357
MEF2C Layer 4 2.9668 0.7351
BSCL2 Layer 2 2.3965 0.7342
PREPL Layer 4 2.3711 0.7336
TAGLN3 Layer 4 2.3711 0.7327
GUCY1B1 Layer 4 2.4727 0.7324
LMO4 Layer 4 2.4668 0.7315
EEF1A2 Layer 4 2.3809 0.7311
ENO2 Layer 3 2.2461 0.7306
ATP1A3 Layer 4 2.5957 0.7305
ATP1B1 Layer 3 2.0859 0.7303
ARHGDIG Layer 5 2.3496 0.7293
INA Layer 3 2.8906 0.7291
SYP Layer 4 2.6309 0.7288
CNTN1 Layer 5 2.2969 0.7287
SIRPA Layer 2 2.3994 0.7282
CLTC Layer 3 2.2969 0.7268
ATP6V1B2 Layer 5 2.5059 0.7267
MAGED1 Layer 4 2.4395 0.7265
USP11 Layer 4 2.5566 0.7263
USP22 Layer 4 2.5215 0.7262
SYN1 Layer 4 2.4395 0.7258
PHYHIP Layer 2 2.6719 0.7257
RGS4 Layer 5 2.4336 0.7254
FXYD7 Layer 4 2.5957 0.7253

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1726
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1726_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1726/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1726/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1726/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1726/report/PD/BN1726_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1726/report/PD/BN1726_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 06:03:51
  • Number of Processes: 10
  • Spending Time: 0h 3m